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Merge branch 'releases/Release_2_11_1_Branch' of http://source.jalview.org/git/jalvie...
authorJim Procter <jprocter@issues.jalview.org>
Wed, 21 Oct 2020 15:21:28 +0000 (16:21 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Wed, 21 Oct 2020 15:21:28 +0000 (16:21 +0100)
RELEASE patch | blob | history
help/help/html/releases.html patch | blob | history
help/help/html/whatsNew.html patch | blob | history
src/jalview/analysis/Finder.java patch | blob | history
test/jalview/analysis/FinderTest.java patch | blob | history

diff --git a/RELEASE b/RELEASE
index 90eaa35..b5ce6d5 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
 jalview.release=releases/Release_2_11_1_Branch
-jalview.version=2.11.1.2
+jalview.version=2.11.1.3
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 9d3c0d2..0e3e652 100755 (executable)
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -57,6 +57,23 @@ li:before {
     </tr>
     <tr>
       <td width="60" align="center" nowrap><strong><a
+          id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
+          <em>27/10/2020</em></strong></td>
+      <td align="left" valign="top">
+        <ul>
+        </ul>
+      </td>
+      <td align="left" valign="top">
+        <ul>
+          <li>
+            <!-- JAL-3765 -->Find doesn't always highlight all matching
+            positions in a sequence
+          </li>
+        </ul>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" align="center" nowrap><strong><a
           id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
           <em>25/09/2020</em></strong></td>
       <td align="left" valign="top">
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index cc91c62..a448aaa 100755 (executable)
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -24,9 +24,9 @@
 </head>
 <body>
   <p>
-    <strong>Jalview 2.11.1.2</strong>
+    <strong>Jalview 2.11.1.3</strong>
   </p>
-  <p>Jalview 2.11.1.2 is the second patch release, fixing a bug
+  <p>Jalview 2.11.1.3 is the third patch release, fixing a bug
     introduced in last weeks Jalview 2.11.1.1 release affecting display
     of Jalview's example project for some users. Together, these
     releases include fixes for a number of critical bugs, and also contains a
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index c545c7f..d52e42a 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -417,7 +417,7 @@ public class Finder implements FinderI
      * update residueIndex to next position after the start of the match
      * (findIndex returns a value base 1, columnIndex is held base 0)
      */
-    residueIndex += offset + 1;
+    residueIndex = searchPattern.matchedFrom()+1;
 
     /*
      * return false if the match is entirely in a hidden region
diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 95e6c0d..1f45f70 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -123,6 +123,19 @@ public class FinderTest
     assertEquals(matches.get(1).getEnd(), 6);
   }
 
+  @Test(groups = "Functional")
+  public void testFind_findAll()
+  {
+    /*
+     * simple JAL-3765 test
+     * single symbol should find *all* matching symbols 
+     */
+    Finder f = new Finder(av);
+    f.findAll("M", false,false,false);
+    SearchResultsI sr = f.getSearchResults();
+    assertEquals(sr.getCount(),5);
+    
+  }
   /**
    * Test for (undocumented) find residue by position
    */